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'''BD_BOX''' <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, | '''BD_BOX''' <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734–2744 (2011)]</ref> | ||
BD_BOX uses [[Flexible molecules |flexible]] | is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms. BD_BOX uses [[Flexible molecules |flexible]] bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Non-bonded potentials include pairwise functions describing screened [[electrostatics]] in dielectric media and [[Lennard-Jones model |Lennard-Jones functions]]. Hydrodynamically correlated motions of particles are modelled using configuration-dependent [[diffusion]] tensors. Brownian dynamics simulations can be performed either for single molecules or [[Periodic boundary conditions |periodic]] multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU. | ||
BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU. | Work on BD_BOX is supported by Polish National Science Centre. | ||
==References== | ==References== | ||
<references/> | <references/> | ||
==External links== | ==External links== | ||
*[http:// | *[http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page] | ||
[[Category: Materials modelling and computer simulation codes]] | [[Category: Materials modelling and computer simulation codes]] |